Search for Variation information by Variation ID:
Detailed information for vg0819106870:
| Variant ID: vg0819106870 (JBrowse) | Variation Type: SNP |
| Chromosome: chr08 | Position: 19106870 |
| Reference Allele: C | Alternative Allele: T,G |
| Primary Allele: C | Secondary Allele: T |
Inferred Ancestral Allele: Not determined.
Flanking Sequence (100 bp) in Reference Genome:
TTCAACTTCCTGCTGGCCATACAATCCCATTGGCTGAAGAATTGGGCAAGAGGAGATATTATAAGTGGCATAATTTTGGGTCTCATTCCACCAATGTTTG[C/T,G]
AAGGTCTTCAGGCAGCAGATCCAAGCAGCTATTGAGGGAGGCAAAATCAAATTTGATGATTCTAAGAGGCCGATGAAGGTTGATGGCAATCCTTTTCCTG
Reverse complement sequence
CAGGAAAAGGATTGCCATCAACCTTCATCGGCCTCTTAGAATCATCAAATTTGATTTTGCCTCCCTCAATAGCTGCTTGGATCTGCTGCCTGAAGACCTT[G/A,C]
CAAACATTGGTGGAATGAGACCCAAAATTATGCCACTTATAATATCTCCTCTTGCCCAATTCTTCAGCCAATGGGATTGTATGGCCAGCAGGAAGTTGAA
Allele Frequencies:
| Populations | Population Size | Frequency of C(primary allele) | Frequency of T(secondary allele) | Frequency of N | Frequency of DEL | Frequency of others Allele |
|---|---|---|---|---|---|---|
| All | 4726 | 78.60% | 1.40% | 17.54% | 2.18% | G: 0.25% |
| All Indica | 2759 | 71.40% | 1.70% | 25.05% | 1.38% | G: 0.43% |
| All Japonica | 1512 | 88.60% | 1.10% | 6.55% | 3.77% | NA |
| Aus | 269 | 91.10% | 0.40% | 8.55% | 0.00% | NA |
| Indica I | 595 | 65.40% | 1.30% | 32.61% | 0.67% | NA |
| Indica II | 465 | 67.30% | 0.40% | 27.53% | 4.09% | G: 0.65% |
| Indica III | 913 | 76.90% | 3.30% | 19.28% | 0.22% | G: 0.33% |
| Indica Intermediate | 786 | 72.10% | 0.90% | 24.55% | 1.65% | G: 0.76% |
| Temperate Japonica | 767 | 99.70% | 0.00% | 0.13% | 0.13% | NA |
| Tropical Japonica | 504 | 69.40% | 3.00% | 17.86% | 9.72% | NA |
| Japonica Intermediate | 241 | 92.90% | 0.80% | 3.32% | 2.90% | NA |
| VI/Aromatic | 96 | 96.90% | 0.00% | 3.12% | 0.00% | NA |
| Intermediate | 90 | 75.60% | 1.10% | 14.44% | 8.89% | NA |
Allele Effect:
| Var ID | Var | Locus | snpEff Annotation | CooVar Annotation | Chromatin Accessibility Score | PolyPhen-2 Effect | PolyPhen-2 Score | SIFT Effect | SIFT Score |
|---|---|---|---|---|---|---|---|---|---|
| vg0819106870 | C -> G | LOC_Os08g30940.1 | missense_variant ; p.Cys455Trp; MODERATE | nonsynonymous_codon ; C455W | Average:12.75; most accessible tissue: Callus, score: 27.742 | probably damaging  |
3.518 |
DELETERIOUS | 0.01 |
| vg0819106870 | C -> T | LOC_Os08g30940.1 | synonymous_variant ; p.Cys455Cys; LOW | synonymous_codon | Average:12.75; most accessible tissue: Callus, score: 27.742 | N | N | N | N |
| vg0819106870 | C -> DEL | LOC_Os08g30940.1 | N | frameshift_variant | Average:12.75; most accessible tissue: Callus, score: 27.742 | N | N | N | N |
Putative Genotype-Phenotype Associations:
| Var ID | LMM P-value | LR P-value | Trait | Subpopulation | Is leadSNP | Publication |
|---|---|---|---|---|---|---|
| vg0819106870 | 6.48E-07 | 6.48E-07 | mr1666_2 | Ind_All | YES | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |
| vg0819106870 | 7.01E-06 | 7.01E-06 | mr1770_2 | Ind_All | Not | Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism, Nat Genet, 46(7):714-21, PMID:24908251 |